For example, 外 can be read がい and そと on its own. 人 can be read じん / にん and ひと. 日 can be readじつ / にち and ひ. So that begs the question, when to use which? Does it depend on context? I know that when paired with other kanji/hiragana, it will use a specific reading. Such as 外人 always being read がいじん. But… what if they’re on their own? Sure, WaniKani says “Vocabulary Reading” and “Kanji Reading”, but regular Japanese people don’t write “Read this kanji がい.” I’m sure that almost nobody sane would. But, my question is, (again) When do I use the おんよみ reading and when to use the くんよみ reading?
If it’s on its own, then it’s the kun’yomi reading. So, 外, 人, 日. Verbs and adjectives also use the kun’yomi. If it’s a compound word, it’s usually gonna be the on’yomi. Most compound words will use on’yomi, some will use kun’yomi, and few will use a mix of both; you’ll just have to get a feel for them
You seem to be still a bit confused about the difference between Kanji and Words.
Words (what wanikani shows as purple) have a correct reading. They appear in the wild and you are expected to know their reading, or at least the more common ones.
Kanji (what wanikani shows as pink) are just letters, and thus can be used in many different ways to produce different sounds (god knows how many ways one can pronounce the letter “a” in English, lol). When learning Japanese we study those because they are useful, but by definition they do not appear on the wild.
What causes confusion is that some letters (the three you gave, for exemple) can be used as one-letter words. But the same is true for English. While the letters “a” and “i” can have several pronunciations, the words “a” and “I” clearly have one correct pronunciation.
What’s the reading of 外？
I don’t know, man. It can be がい、そと、げ、はず、who knows.
What’s the reading of 外で待っています
Oh, that’s 100% そと, because “がい” is not a word that exists in Japanese.
Long story short:
Care about answering the purple cards readings correctly. The pink ones, as long as you give one correct answer, it should be fine.
The patterns for what’s on and what’s kun come rather naturally later on.
General rule of thumb, use the one that came up as a vocab lesson, that for sure works. Onyomi readings are restricted to compounds mainly